BRC

Plot aa similarity clonotypes cohort 1

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="patient_id", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'Patient_clonotype' as categorical
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'expansion_on' as categorical
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'E2F4_activity' as categorical

<matplotlib.axes._subplots.AxesSubplot at 0x7f01511b45b0>

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="timepoint", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01510e07f0>

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="cell_type", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01510b4820>

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="expansion_on", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0197f82820>

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="expansion", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01fd656910>

# VDJDB antigen annotation
ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="VDJdb", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f016d97a2b0>

# IEDB antigen annotation
ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="IEDB", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01f73d2a60>

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="E2F4_score", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01f73d2910>

ir.pl.clonotype_network(
    adata_cohort_1_aa,  color="E2F4_activity", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01f80a6c10>

Plot aa similarity clonotypes cohort 2

ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="patient_id", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'Patient_clonotype' as categorical
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'expansion_on' as categorical

<matplotlib.axes._subplots.AxesSubplot at 0x7f0104af87c0>

ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="timepoint", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f013934f970>

ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="cell_type", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0105c55ee0>

ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="expansion_on", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f01f40fea00>

ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="expansion", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0232b31250>

# VDJDB antigen annotation
ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="VDJdb", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0236017700>

# IEDB antigen annotation
ir.pl.clonotype_network(
    adata_cohort_2_aa,  color="IEDB", base_size=10, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0236d71160>

LUNG

Plot aa similarity clonotype networks

ir.pl.clonotype_network(
    adata_aa,  color="patient_id", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'Patient_clonotype' as categorical
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'expansion_on' as categorical
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'E2F4_activity' as categorical

<matplotlib.axes._subplots.AxesSubplot at 0x7f08c42bc670>

ir.pl.clonotype_network(
    adata_aa,  color="timepoint", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f09090f77f0>

ir.pl.clonotype_network(
    adata_aa,  color="response", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0908fbf400>

ir.pl.clonotype_network(
    adata_aa,  color="cell_type", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f0908fb7ee0>

ir.pl.clonotype_network(
    adata_aa,  color="expansion_on", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f08c26548e0>

ir.pl.clonotype_network(
    adata_aa,  color="VDJdb", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f08adfaabb0>

ir.pl.clonotype_network(
    adata_aa,  color="IEDB", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f091ecc8ca0>

ir.pl.clonotype_network(
    adata_aa,  color="E2F4_score", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f091db90700>

ir.pl.clonotype_network(
    adata_aa,  color="E2F4_activity", base_size=3, label_fontsize=9, panel_size=(7, 7)
)

<matplotlib.axes._subplots.AxesSubplot at 0x7f091de60d00>